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<CHAPTER ID="MAINWINDOW-CHAPTER">
  <TITLE>The &prog; Main Window</TITLE>

  <SECT1 ID="MAINWINDOW-OVERVIEW">
    <TITLE>Overview of the Entry Edit Window</TITLE>
    <PARA>
This window is the main editing and viewing window. See <XREF
LINKEND="LAUNCH-WINDOW-FILE-MENU-OPEN"> or <XREF
LINKEND="LAUNCH-WINDOW-FILE-MENU-READ-FROM-EBI"> to find out how to read an
entry (and hence open one of these windows).
    </PARA>

    <PARA>
The following images show a breakdown of the main &prog; edit window. The full
screen shot <ULINK
URL="user_manual_screen_shot.gif"
TYPE="external">is here</ULINK>.
    </PARA>

    <SECT2 ID="MAINWINDOW-BREAKDOWN">
      <TITLE>A breakdown of the main &prog; edit window</TITLE>

      <ORDEREDLIST ID="MAINWINDOW-BREAKDOWN-LIST">
        <LISTITEM ID="MAINWINDOW-BREAKDOWN-MENU">
        <PARA>
          <SCREENSHOT>
            <SCREENINFO>
The menu bar of the main &prog; window
            </SCREENINFO>
            <MEDIAOBJECT>
              <IMAGEOBJECT>
                <IMAGEDATA FORMAT="png" FILEREF="main_window_1.png">
              </IMAGEOBJECT>
              <IMAGEOBJECT>
                <IMAGEDATA FORMAT="eps" FILEREF="main_window_1.eps">
              </IMAGEOBJECT>
            </MEDIAOBJECT>
          </SCREENSHOT>
          </PARA>
        </LISTITEM>

        <LISTITEM ID="MAINWINDOW-BREAKDOWN-SELECTIONSTATUS">
        <PARA>
          <SCREENSHOT>
            <SCREENINFO>
A one line summary of the what is currently selected
            </SCREENINFO>
            <MEDIAOBJECT>
              <IMAGEOBJECT>
                <IMAGEDATA FORMAT="png" FILEREF="main_window_2.png">
              </IMAGEOBJECT>
              <IMAGEOBJECT>
                <IMAGEDATA FORMAT="eps" FILEREF="main_window_2.eps">
              </IMAGEOBJECT>
            </MEDIAOBJECT>
          </SCREENSHOT>
        </PARA>
        </LISTITEM>
        
        <LISTITEM ID="MAINWINDOW-BREAKDOWN-ENTRY-BUTTONS">
        <PARA>
          <SCREENSHOT>
            <SCREENINFO>
The entry buttons from the main &prog; window
            </SCREENINFO>
            <MEDIAOBJECT>
              <IMAGEOBJECT>
                <IMAGEDATA FORMAT="png" FILEREF="main_window_3.png">
              </IMAGEOBJECT>
              <IMAGEOBJECT>
                <IMAGEDATA FORMAT="eps" FILEREF="main_window_3.eps">
              </IMAGEOBJECT>
            </MEDIAOBJECT>
          </SCREENSHOT>
        </PARA>
        </LISTITEM>
        
        <LISTITEM ID="MAINWINDOW-BREAKDOWN-OVERVIEW">
          <PARA>
          <SCREENSHOT>
            <SCREENINFO>
The sequence overview
            </SCREENINFO>
            <MEDIAOBJECT>
              <IMAGEOBJECT>
                <IMAGEDATA FORMAT="png" FILEREF="main_window_4.png">
              </IMAGEOBJECT>
              <IMAGEOBJECT>
                <IMAGEDATA FORMAT="eps" FILEREF="main_window_4.eps">
              </IMAGEOBJECT>
            </MEDIAOBJECT>
          </SCREENSHOT>
          </PARA>
        </LISTITEM>
        
        <LISTITEM ID="MAINWINDOW-BREAKDOWN-DNAVIEW">
          <PARA>
          <SCREENSHOT>
            <SCREENINFO>
The DNA view
            </SCREENINFO>
            <MEDIAOBJECT>
              <IMAGEOBJECT>
                <IMAGEDATA FORMAT="png" FILEREF="main_window_5.png">
              </IMAGEOBJECT>
              <IMAGEOBJECT>
                <IMAGEDATA FORMAT="eps" FILEREF="main_window_5.eps">
              </IMAGEOBJECT>
            </MEDIAOBJECT>
          </SCREENSHOT>
          </PARA>
        </LISTITEM>
        
        <LISTITEM ID="MAINWINDOW-BREAKDOWN-FEATURELIST">
          <PARA>
          <SCREENSHOT>
            <SCREENINFO>
The feature list
            </SCREENINFO>
            <MEDIAOBJECT>
              <IMAGEOBJECT>
                <IMAGEDATA FORMAT="png" FILEREF="main_window_6.png">
              </IMAGEOBJECT>
              <IMAGEOBJECT>
                <IMAGEDATA FORMAT="eps" FILEREF="main_window_6.eps">
              </IMAGEOBJECT>
            </MEDIAOBJECT>
          </SCREENSHOT>
          </PARA>
        </LISTITEM>
      </ORDEREDLIST>
      <PARA>
Key:
      </PARA>
      <ORDEREDLIST ID="MAINWINDOW-INFO">
        <LISTITEM ID="MAINWINDOW-INFO-MENU">
          <PARA>
The menus for the main window (described later in this chapter).
          </PARA>
        </LISTITEM>
        <LISTITEM ID="MAINWINDOW-INFO-SELECTIONSTATUS">
          <PARA>
A one line summary of the current selection (see <XREF LINKEND="SELECTMENU">
and <XREF LINKEND="CONCEPTS-SELECTION"> for more).
          </PARA>
        </LISTITEM>
        <LISTITEM ID="MAINWINDOW-INFO-ENTRYBUTTONS">
          <PARA>
This line contains one button for each entry that has been loaded. These
buttons allow the user to set the default entry (see <XREF
LINKEND="CONCEPTS-DEFAULTENTRY">) and to set the active entries
(see <XREF LINKEND="CONCEPTS-ACTIVEENTRY">).
For more detail on operating the buttons see <XREF
LINKEND="ENTRYBUTTONS">.
          </PARA>
        </LISTITEM>
        <LISTITEM ID="MAINWINDOW-INFO-OVERVIEW">
          <PARA>
This shows an overview of the sequence and the features from the active
entries. (see <XREF LINKEND="VIEWS">).
          </PARA>
        </LISTITEM>
        <LISTITEM ID="MAINWINDOW-INFO-DNAVIEW">
          <PARA>
This is called the "DNA view" to distinguish it from the overview, but in fact
it operates in a very similar way. (see <XREF LINKEND="VIEWS">).
          </PARA>
        </LISTITEM>
        <LISTITEM ID="MAINWINDOW-INFO-FEATURELIST">
          <PARA>
A textual summary of the active features. (See <XREF
LINKEND="FEATURELIST">).
          </PARA>
        </LISTITEM>
      </ORDEREDLIST>
    </SECT2>
  </SECT1>

  &filemenu;
  &menus;
  &displaymenu;

  <SECT1 ID="ENTRYBUTTONS">
    <TITLE>The Entry Button Line</TITLE>
    <PARA>
There is one button on this line for each currently loaded entry. The buttons
indicate which entries are active and allow the user to toggle each entry
between the active and inactive states. The default entry can be set by
clicking the right mouse button (see <XREF LINKEND="MOUSEBUTTONS">) on an
entry.
    </PARA>
    <PARA>
See also <XREF LINKEND="MAINWINDOW-BREAKDOWN-ENTRY-BUTTONS">, <XREF
LINKEND="CONCEPTS-DEFAULTENTRY"> and <XREF LINKEND="CONCEPTS-ACTIVEENTRY">).
    </PARA>
  </SECT1>

  <SECT1 ID="VIEWS">
    <TITLE>The Overview and DNA Views</TITLE>
    <PARA>
The overview and DNA view take up most of the main window (see <XREF
LINKEND="MAINWINDOW-BREAKDOWN">). Both views act in a very similar way, so
they are described in the same section. In particular they both show the
forward and reverse strands of the sequence and a representation of the three
translation frames in each direction. The forward sequence is read from
the EMBL entry, the reverse sequence is derived from the forward one by
complementing it. In the overview shows only the stop codons of each
translation frame, but in the DNA view the shows the complete six frame
translation.
    </PARA>
    <PARA>
The horizontal scrollbar controls which part of the sequence is
currently visible. The scroll bar at the left controls the zoom level.
    </PARA>

&views-selection;

    <SECT2 ID="VIEWS-OTHERMOUSE">
      <TITLE>Other Mouse Controlled Functions</TITLE>
      <PARA>
Double clicking on a feature with the first mouse button causes both views and
the feature list to centre themselves on that feature. Similarly, double
clicking the first mouse button on a base or amino acid will centre both views
on that base/amino acid.
      </PARA>
      <PARA>
A double click of the middle mouse button on a feature will open an edit
window for that feature. This is the same as clicking once and then choosing
the Edit Selected Features menu item (see <XREF
LINKEND="EDITMENU-EDIT-SELECTED-FEATURES">).
      </PARA>
    </SECT2>

&views-popup;
&views-scrolling;
&views-scale;
&views-directedit;
  </SECT1>

&featurelist;

  <SECT1 ID="GRAPHS">
    <TITLE>Graphs and Plots</TITLE>
    <PARA>
The DNA plots are accessed from the Graph menu (see <XREF
LINKEND="GRAPHMENU">). When a graph is turned on it is locked to the
overview window, so it will follow the overview window when the overview is
scrolled. It will also automatically change the viewing scale to match the
scale of the overview window. The vertical scrollbar to the right of the
graph controls the window size of algorithm.
    </PARA>

    <PARA>
The feature plots window (see <XREF LINKEND="VIEWMENU-SHOW-FEATURE-PLOTS">)
has a horizontal scroll bar that sets the position of the plot in the feature.
As with the DNA plots, the vertical scrollbar to the right of the graph
controls the window size of algorithm.
    </PARA>

    <PARA>
Note that clicking the left mouse button on the plot will show the base or
residue at that position. Clicking the right mouse button will pop-up a menu.
The menu contains a toggle which controls whether the graph is scaled and some
menu items which allow the maximum window size to be set.
    </PARA>
  </SECT1>

&validator;
&mousebuttons;
</CHAPTER>
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